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Yorodumi- PDB-2yrx: Crystal structure of GAR synthetase from Geobacillus kaustophilus -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yrx | ||||||
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Title | Crystal structure of GAR synthetase from Geobacillus kaustophilus | ||||||
Components | Phosphoribosylglycinamide synthetase | ||||||
Keywords | LIGASE / Glycinamide ribonucleotide synthetase / GAR synthetase / ATP binding / Purine nucleotide biosynthetic pathway / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / purine nucleobase biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Baba, S. / Kanagawa, M. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biochem. / Year: 2010 Title: Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria Authors: Sampei, G. / Baba, S. / Kanagawa, M. / Yanai, H. / Ishii, T. / Kawai, H. / Fukai, Y. / Ebihara, A. / Nakagawa, N. / Kawai, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yrx.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yrx.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 2yrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yrx_validation.pdf.gz | 784.3 KB | Display | wwPDB validaton report |
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Full document | 2yrx_full_validation.pdf.gz | 790.3 KB | Display | |
Data in XML | 2yrx_validation.xml.gz | 19 KB | Display | |
Data in CIF | 2yrx_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/2yrx ftp://data.pdbj.org/pub/pdb/validation_reports/yr/2yrx | HTTPS FTP |
-Related structure data
Related structure data | 2ip4C 2yrwSC 2ys6C 2ys7C 2yw2C 2yyaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48228.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli) References: UniProt: Q5L3C7, phosphoribosylamine-glycine ligase | ||||
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#2: Chemical | #3: Chemical | ChemComp-AMP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2M ammonium sulfate, 0.1M sodium acetate trihydrate, 30% polyethylene glycol monomethyl ether 2000, 10mM ATP, pH4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 23, 2006 |
Radiation | Monochromator: Fixed exit Si 111 double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 32811 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.102 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.655 / Num. unique all: 3204 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YRW Resolution: 1.9→48.23 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 73409.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.1105 Å2 / ksol: 0.369089 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→48.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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